Package readmzxmldata

Transcription

1 Version 2.7 Date Package readmzxmldata July 3, 2013 Title Reads mass spectrometry data in mzxml format Depends R (>= ) Imports base64enc, digest, XML Suggests MALDIquant (>= 1.0) Functions for reading mass spectrometry data in mzxml format. License GPL (>= 3) URL BugReports LazyLoad yes Collate attribute-functions.r base64-functions.r grep-functions.r mqreadmzxmlfunctions.r package.r parsemzxml.r readmzxmldir-functions.r readmzxmlfilefunctions.r revfregexpr-functions.r Author Sebastian Gibb [aut, cre] Maintainer NeedsCompilation no Repository CRAN Date/Publication :44:42 R topics documented: readmzxmldata-package mqreadmzxml readmzxmldir readmzxmlfile Index 7 1

2 2 mqreadmzxml readmzxmldata-package The readmzxmldata Package The package reads mass spectrometry data in mzxml format. Details Package: readmzxmldata Type: Package Version: 2.7 Date: License: GPL(version 3 or later) Main functions: readmzxmlfile: Reads mass spectrometry data in mzxml format. readmzxmldir: Reads recursively mass spectrometry data in mzxml format in a specific directory. mqreadmzxml: Reads mass spectrometry data into MALDIquant. References See website: readmzxmldir, readmzxmlfile, mqreadmzxml mqreadmzxml Reads mass spectrometry data into MALDIquant. This function is deprecated and will be removed in the next release. Use importmzxml instead. Reads all mass spectrometry data in mzxml format in a specified path into MALDIquant-package MassSpectrum-class objects.

3 readmzxmldir 3 Usage mqreadmzxml(path,...) Arguments path character, path to directory or a single mzxml file.... arguments to be passed to readmzxmldir or readmzxmlfile. Details See readmzxmldir or readmzxmlfile for details. Value Returns a list of MassSpectrum-class objects. References See website: readmzxmldir, readmzxmlfile, MALDIquant-package, MassSpectrum-class readmzxmldir Reads recursively mass spectrometry data in mzxml format. Reads recursively all mass spectrometry data in mzxml format in a specified directory. Usage readmzxmldir(mzxmldir, removecalibrationscans = TRUE, removemetadata = FALSE, rewritenames = TRUE, fileextension = "mzxml", verbose = FALSE)

4 4 readmzxmldir Arguments Details Value mzxmldir character, path to directory which should be read recursively. removecalibrationscans logical, if TRUE all scans in directories called [Cc]alibration will be ignored. removemetadata logical, to save memory metadata could be deleted. rewritenames fileextension verbose See readmzxmlfile. A list of spectra. logical, if TRUE all list elements get an unique name from metadata otherwise file path is used. character, file extension of mzxml formatted files. The directory is only searched for fileextension files. In most cases it would be "mzxml" but sometimes you have to use xml. logical, verbose output? [[1]]spectrum$mass: A vector of calculated mass. [[1]]spectrum$intensity: A vector of intensity values. [[1]]metaData: A list of metadata depending on read spectrum. readmzxmlfile, mqreadmzxml Examples ## load library library("readmzxmldata") ## get examples directory exampledirectory <- system.file("examples", package="readmzxmldata") ## read example spectra spec <- readmzxmldir(exampledirectory) ## plot spectra plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n") l <- length(spec) legendstr <- character(l) for (i in seq(along=spec)) {

5 readmzxmlfile 5 lines(spec[[i]]$spectrum$mass, spec[[i]]$spectrum$intensity, type="l", col=rainbow(l)[i]) legendstr[i] <- basename(spec[[i]]$metadata$file) } ## draw legend legend(x="topright", legend=legendstr, col=rainbow(l), lwd=1) readmzxmlfile Reads mass spectrometry data in mzxml format. Reads mass spectrometry data in mzxml format defined in org/mzxmlschema.php. Usage readmzxmlfile(mzxmlfile, removemetadata = FALSE, verbose = FALSE) Arguments mzxmlfile character, path to mzxml file which should be read. removemetadata logical, to save memory metadata could be deleted. verbose logical, verbose output? Value A list of spectra and metadata. spectrum$mass: A vector of calculated mass. spectrum$intensity: A vector of intensity values. metadata: A list of metadata depending on read spectrum. References Definition of mzxml format: readmzxmldir, mqreadmzxml

6 6 readmzxmlfile Examples ## load library library("readmzxmldata") ## get examples directory exampledirectory <- system.file("examples", package="readmzxmldata") ## read example spectrum spec <- readmzxmlfile(file.path(exampledirectory, "A1-0_A1.mzXML")) ## print metadata print(spec$metadata) ## plot spectrum plot(spec$spectrum$mass, spec$spectrum$intensity, type="l")

7 Index Topic IO mqreadmzxml, 2 readmzxmldata-package, 2 readmzxmldir, 3 readmzxmlfile, 5 importmzxml, 2 mqreadmzxml, 2, 2, 4, 5 mqreadmzxml-deprecated (mqreadmzxml), 2 readmzxmldata-package, 2 readmzxmldir, 2, 3, 3, 5 readmzxmlfile, 2 4, 5 7